UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-K/A

(Amendment No. 1)

(Mark One)

For the Year Ended December 31, 2012

or

For the transition period from              to             

Commission File Number: 001-33466

PATRIOT COAL CORPORATION

(Exact name of registrant as specified in its charter)

(314) 275-3600

(Registrant’s telephone number, including area code)

Securities Registered Pursuant to Section 12(b) of the Act:

None.

Securities Registered Pursuant to Section 12(g) of the Act:

Common Stock, par value $0.01 per share

Preferred Share Purchase Rights

Indicate by check mark if the registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act    Yes  ¨    No  þ

Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act    Yes  ¨    No  þ

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days.    Yes  þ    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).    Yes  þ    No  ¨

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  ¨

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act)    Yes  ¨    No  þ

Aggregate market value of the voting stock held by non-affiliates (shareholders who are not directors or executive officers) of the Registrant, calculated using the closing price on June 29, 2012: Common Stock, par value $0.01 per share, $111.6 million.

Number of shares outstanding of each of the Registrant’s classes of Common Stock, as of April 25, 2013: Common Stock, par value $0.01 per share, 92,398,668 shares outstanding.

DOCUMENTS INCORPORATED BY REFERENCE:

None

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-K/A (this “Amendment”) amends our Annual Report on Form 10-K for the fiscal year ended December 31, 2012, that was filed with the Securities and Exchange Commission (“SEC”) on February 22, 2013 (the “Form 10-K”). We are filing this Amendment to provide the information required by Part III of our Form 10-K. The Amendment also updates the information on the cover page of the Form 10-K with respect to the Company’s outstanding common stock registered under Section 12(g) of the Securities Exchange Act of 1934, as amended. The Form 10-K continues to speak as of the date of the Form 10-K. Unless expressly stated, this Amendment does not reflect events occurring after the filing of the Form 10-K, nor does it modify or update in any way the disclosures contained in the Form 10-K.

On July 9, 2012, Patriot Coal Corporation (“Patriot” or the “Company”) and substantially all of its subsidiaries filed for protection under Chapter 11 of Title 11 of the U.S. Code (the “Bankruptcy Code”) in the Bankruptcy Court for the Southern District of New York. On November 27, 2012, the Bankruptcy Court for the Southern District of New York ordered that the bankruptcy cases be transferred to the Bankruptcy Court for the Eastern District of Missouri, and on December 19, 2012, the Bankruptcy Court for the Southern District of New York entered an order transferring the bankruptcy cases to the Bankruptcy Court for the Eastern District of Missouri (the “Bankruptcy Court”), effective as of that date.

Unless otherwise indicated, any descriptions of executory contracts in this Amendment do not give effect to the Chapter 11 filing and must be read in conjunction with, and are qualified by, any applicable provisions under the Bankruptcy Code.

TABLE OF CONTENTS

CAUTIONARY NOTICE REGARDING FORWARD-LOOKING STATEMENTS

This report and other materials filed or to be filed by Patriot Coal Corporation include statements of our expectations, intentions, plans and beliefs that constitute “forward-looking statements” within the meaning of Section 27A of the Securities Act of 1933 and Section 21E of the Securities Exchange Act of 1934 and are intended to come within the safe harbor protection provided by those sections. You can identify these forward-looking statements by the use of forward-looking words such as “outlook,” “believes,” “expects,” “potential,” “continues,” “may,” “will,” “should,” “seeks,” “approximately,” “predicts,” “intends,” “plans,” “estimates,” “anticipates,” “foresees” or the negative version of those words or other comparable words and phrases. Any forward-looking statements contained in this report are based upon our historical performance and on current plans, estimates and expectations. The inclusion of this forward-looking information should not be regarded as a representation by us or any other person that the future plans, estimates or expectations contemplated by us will be achieved.

PART III

ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE

BOARD OF DIRECTORS

J. JOE ADORJAN, age 74, has been a director of the Company since November 2007. Mr. Adorjan is currently Chairman of Adven Capital, a private equity firm, and Chairman of Bates Sales Company, a distributor of industrial power transmission equipment and parts. He has served in these positions since February 2001. From 1995 through December 2000, Mr. Adorjan served as Chairman and Chief Executive Officer of Borg-Warner Security Corporation, a provider of security services. Prior to joining Borg-Warner, Mr. Adorjan served in a number of senior executive capacities with Emerson Electric Co. and ESCO Electronics Corporation, an independent New York Stock Exchange-listed (the “NYSE”) corporation that was formed in 1990 in connection with the spin-off of Emerson’s government and defense business. He was Chairman and Chief Executive Officer of ESCO from 1990 to 1992. Mr. Adorjan originally joined Emerson in 1968 and served in a number of senior executive capacities, including Executive Vice President of Finance, International, Technology and Corporate Development.

Mr. Adorjan has a Bachelor’s and Master’s degree in Economics from Saint Louis University. Mr. Adorjan serves on the board of trustees of Saint Louis University and Ranken Technical College and is Chairman of The Hungarian-Missouri Educational Partnership. Mr. Adorjan previously served as a director of Rexel Corporation (2008-2011) and Thermadyne Holdings Corporation (2005-2010) where he served as lead director and as a member of the audit and compensation committees.

We believe Mr. Adorjan’s qualifications to sit on our Board of Directors (the “Board”) include his experience as an executive leader of complex organizations and experience as a director of other companies.

B. R. BROWN, age 80, has been a director of the Company since October 2007. Mr. Brown is the retired Chairman, President and Chief Executive Officer of CONSOL Energy, Inc., a domestic coal and gas producer and energy services provider. He served as Chairman, President and Chief Executive Officer of CONSOL and predecessor companies from 1978 to 1998. He also served as a Senior Vice President of E.I. du Pont de Nemours & Co., CONSOL’s controlling stockholder, from 1981 to 1991. Before joining CONSOL, Mr. Brown was a Senior Vice President at Conoco. From 1990 to 1995, he also was President and Chief Executive Officer of Remington Arms Company, Inc.

Mr. Brown has a Bachelor’s degree in Economics from the University of Arkansas. Mr. Brown is currently a director of Delta Trust & Bank and Remington Arms Company, Inc. and its parent, Freedom Group, Inc. He has previously served as a director and Chairman of the Bituminous Coal Operators’ Association Negotiating Committee, Chairman of the National Mining Association (“NMA”) and Chairman of the Coal Industry Advisory Board of the International Energy Agency. Mr. Brown was a director of Peabody Energy Corporation (“Peabody”) from December 2003 until October 2007, when he resigned to join the Board.

We believe Mr. Brown’s qualifications to sit on the Board include his experience in the coal industry, his executive leadership of complex organizations and his experience as a director of other companies.

BENNETT K. HATFIELD, age 56, has been a director of the Company since October 2012. Mr. Hatfield has served as President and Chief Executive Officer (“CEO”) of the Company since October 2012. Mr. Hatfield previously served as President and Chief Operating Officer of the Company from May 2012 through October 2012. From September 2011 through May 2012, Mr. Hatfield served as Executive Vice President and Chief Operating Officer of the Company. Prior to joining the Company, Mr. Hatfield served as President, Chief Executive Officer and director of International Coal Group, Inc. from March 2005 until the company was sold in June 2011. Mr. Hatfield previously served as President, Eastern Operations of Arch Coal, Inc. (“Arch”) from March 2003 through March 2005, and Executive Vice President & Chief Commercial Officer of Coastal Coal Company from December 2001 through February 2003. Mr. Hatfield joined Massey Energy Company in 1979, where he served in a number of management roles, most recently as Executive Vice President and Chief Operating Officer from June 1998 through December 2001.

Mr. Hatfield is a board member of the West Virginia Coal Association and the NMA. Mr. Hatfield is a Licensed Professional Engineer with a Bachelor of Science degree in mining engineering from Virginia Polytechnic Institute and State University.

We believe Mr. Hatfield’s qualifications to sit on the Board include his more than thirty years of experience in the coal industry, his leadership and knowledge of the Company, as well as his extensive management experience.

MICHAEL P. JOHNSON, age 65, has been a director of the Company since July 2008. Mr. Johnson has been the President & Chief Executive Officer of J&A Group, a business consulting and investment company, since 2008. He previously served as Senior Vice President and Chief Administrative Officer of The Williams Companies, Inc., a NYSE-listed natural gas producer, processor and transporter, from 1998 to 2008.

Mr. Johnson holds a Bachelor’s degree from North Carolina Central University and is a graduate of the Advanced Executive Program at the Kellogg School of Business at Northwestern University. Mr. Johnson currently serves as a director of QuikTrip Corporation, Buffalo Wild Wings Inc. and CenterPoint Energy, Inc. Mr. Johnson also serves on the boards of Phillips Theological Seminary, the Tulsa Community Foundation and other charitable organizations.

We believe Mr. Johnson’s qualifications to sit on the Board include his management experience in the energy industry and his experience with business and commercial strategy development, information technology and human resources functions.

JANIECE M. LONGORIA, age 59, has been a director of the Company since January 2011. Ms. Longoria has been a partner in the law firm of Ogden, Gibson, Broocks, Longoria & Hall L.L.P. in Houston, Texas since 1997.

Ms. Longoria has a Bachelor’s degree and a Juris Doctorate degree from the University of Texas. Ms. Longoria currently serves as a commissioner of the Port of Houston Authority and serves as a director of CenterPoint Energy, Inc. She previously served as Treasurer and a director of the Houston Convention Center Hotel Corporation (1999-2004) and as a member of The University of Texas System Board of Regents.

We believe Ms. Longoria’s qualifications to sit on the Board include her significant legal experience and background as well as her experience as a director of other institutions.

MICHAEL M. SCHARF, age 65, has been a director of the Company since November 2007 and Chairman of the Board since October 2012. Mr. Scharf also served as Lead Independent Director of the Board from May 2012 to October 2012. Mr. Scharf served as Executive Director, Global Financial Services for Bunge Limited, a global agribusiness and food company (“Bunge”) from January 2010 to July 2011. Previously he was Senior Vice President and Chief Financial Officer of Bunge North America and served in that position from 1990 through 2009. He also served as Bunge’s representative on the board of that company’s biofuels joint ventures. He was previously Senior Vice President and Chief Financial Officer of Peabody Holding Company, Inc. from 1978 to 1990 and Tax Manager at Arthur Andersen & Co. from 1969 to 1978.

Mr. Scharf has a Bachelor’s degree in Accounting from Wheeling Jesuit University and is a certified public accountant. Mr. Scharf currently serves as a director of Renewable Energy Group, Inc.

We believe Mr. Scharf’s qualifications to sit on the Board include his management experience with global companies, his financial expertise and his coal industry experience.

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ROBERT O. VIETS, age 69, has been a director of the Company since November 2007. Mr. Viets is the former President, Chief Executive Officer and director of CILCORP, Inc., a NYSE-listed holding company which owned a regulated electric and natural gas utility (CILCO) in central Illinois. Mr. Viets served in this capacity from 1988 until 1999, when CILCORP was acquired by AES Corporation. He also served as Chief Financial Officer during his 26-year career at CILCORP. Prior to joining CILCORP, Mr. Viets was an auditor with Arthur Andersen & Co. Following his career at CILCORP, Mr. Viets has provided consulting services to regulated energy and communication businesses.

Mr. Viets has a Bachelor’s degree in Economics from Washburn University (Topeka) and a Juris Doctorate degree from Washington University School of Law. He is also a certified public accountant. He has served as a director of, among other companies, RLI Corp., a specialty property and casualty insurer (1993-present), Consumers Water Company, a Maine-based regulated water utility (1996-1998) and Philadelphia Suburban Corp., now Aqua America, Inc. (1998-2001), including serving as a member of the audit committees at RLI Corp. and Philadelphia Suburban Corp.

We believe Mr. Viets’ qualifications to sit on the Board include his experience with electric and gas utilities, his executive leadership of significant organizations and his financial expertise.

CORPORATE GOVERNANCE MATTERS

The Company’s key governance practices are outlined in its Corporate Governance Guidelines, committee charters and Code of Business Conduct and Ethics. These documents can be found on the Company’s website (www.patriotcoal.com) by clicking on “Investors,” and then “Corporate Governance,” and are available in print to any stockholder, without charge, upon request. Information on our website is not considered part of this Amendment. The Code of Business Conduct and Ethics applies to the Company’s directors, CEO, Chief Financial Officer (“CFO”), Controller and other Company personnel. Any updates or amendments to the Code of Business Conduct and Ethics, and any waiver that applies to a director or executive officer, will also be posted on the website.

The Nominating & Governance Committee of the Board (the “Nominating & Governance Committee”) is responsible for reviewing the Corporate Governance Guidelines annually and reporting and making recommendations to the Board concerning corporate governance matters.

AUDIT COMMITTEE

The members of the Audit Committee of the Board (the “Audit Committee”) are Messrs. Viets (Chair), Adorjan and Scharf. The Board has affirmatively determined that, in its judgment, all members of the Audit Committee are independent under NYSE and SEC rules. The Board also has determined that each of Messrs. Viets, Adorjan and Scharf is an “audit committee financial expert” under SEC rules.

Section 16(a) Beneficial Ownership Reporting Compliance

The Company’s executive officers and directors and persons beneficially holding more than 10% of Patriot Common Stock are required under the Securities Exchange Act of 1934, as amended, to file reports of ownership and changes in ownership of Company Common Stock with the SEC. The Company files these reports of ownership and changes in ownership on behalf of its executive officers and directors. To the best of the Company’s knowledge, based solely on its review of the copies of such reports furnished to the Company during the fiscal year ended December 31, 2012, filings with the SEC and written representations from certain reporting persons that no additional reports were required, all required reports were timely filed, except that Mr. Brown inadvertently filed a late Form 4 on December 19, 2012 reporting the sale of Patriot Common Stock on December 12, 2012.

ITEM 11. EXECUTIVE COMPENSATION

EXECUTIVE COMPENSATION

COMPENSATION DISCUSSION AND ANALYSIS

The following discussion provides the framework and analysis of the material elements and objectives of the executive compensation program at Patriot.

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Named Executive Officers for 2012

Our named executive officers for 2012 include the following current executive officers:

In addition, our named executive officers for 2012 include the following former executive officers:

Executive Summary: Chapter 11 Filing and Executive Compensation in 2012

On July 9, 2012, the Company and substantially all of its subsidiaries filed for protection under Chapter 11 of the Bankruptcy Code. Upon Patriot’s Chapter 11 filing, certain incentive programs and certain other aspects of Patriot’s executive compensation program became subject to bankruptcy court approval.

During 2012, the Company’s named executive officers provided significant leadership in stabilizing business operations, obtaining sufficient liquidity to operate the businesses and adjusting to the changes created by the Chapter 11 filing. These leadership efforts included:

Our named executive officers, like our employees generally and our shareholders and other stakeholders, have been significantly impacted by the bankruptcy. Since the Chapter 11 filing, our named executive officers (along with other employees) have had their compensation and benefits materially reduced, as follows:

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Prior to the Chapter 11 filing, other than to satisfy tax withholding obligations upon the vesting of equity awards, only one of the named executive officers ever sold any shares of Patriot Common Stock (i.e., Rule 10b-5 sales totaling 27,143 shares in 2010 and 2011).

Following the Chapter 11 filing, the Company suspended its Long-Term Equity Incentive Plan (the “LTIP”) and anticipates that as part of the bankruptcy process it will terminate the LTIP and cancel outstanding equity awards granted thereunder, and therefore will not grant any new equity awards or issue any shares on settlement or exercise of outstanding equity awards.

Guiding Principles

Prior to the Chapter 11 Filing

In August 2011, the Compensation Committee of the Board (the “Compensation Committee”) approved the guiding principles set forth below, so as to ensure a common understanding of the Company’s executive compensation program among the Compensation Committee and Patriot management. These principles influenced compensation decisions made by the Compensation Committee prior to the Chapter 11 filing, including with respect to the compensation opportunities awarded to the named executive officers in January 2012.

Guiding Principles (as adopted prior to the Chapter 11 filing):

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Since the Chapter 11 Filing

Since the Chapter 11 filing, Patriot has focused on ways to stabilize the business, promote a successful reorganization and preserve jobs by developing a viable business model. Consistent with this focus, Patriot determined to reduce the named executive officers’ compensation and benefits in conjunction with such reductions being sought from all employees. The executives have not and will not receive any annual incentive awards or equity awards during the pendency of the Chapter 11 process, they are no longer eligible to participate in our Supplemental 401(k) Plan and, effective March 1, 2013, their base salaries were reduced by 2.5%.

Roles of the Compensation Committee & the Compensation Consultant

The Compensation Committee is comprised entirely of independent directors and is responsible for the review and approval of the compensation of the Company’s executive officers. The Compensation Committee has overall responsibility for monitoring the performance of the Company’s executive officers and evaluating and approving the Company’s executive compensation plans, policies and programs, including equity compensation, deferred compensation, perquisites, employment agreements, severance arrangements, retirement and other post-employment benefits and change-in-control benefits (in each case, as and when appropriate). In addition, the Compensation Committee oversees the Company’s annual and long-term incentive plans and programs.

The Compensation Committee makes recommendations to the Board regarding the CEO’s compensation, including base salary, annual incentive and long-term incentive compensation and benefits, which recommendations are subject to the approval of the independent members of the Board. The Compensation Committee and the other independent members of the Board also review and approve corporate goals and objectives relevant to such compensation and evaluate the CEO’s performance in light of those goals and objectives.

Under its charter, which can be found on the Company’s website (www.patriotcoal.com), the Compensation Committee has the sole authority to engage the services of outside advisors, experts and others to assist it in fulfilling its duties. The Compensation Committee engaged Towers Watson (referred to herein as the “Consultant”) at the beginning of 2012 to provide compensation consulting advice to the Compensation Committee. The Consultant reports directly to the Compensation Committee, providing the Compensation Committee with advice concerning the types and levels of compensation to be paid to the CEO and the other executive officers of Patriot, including market compensation data on base pay and annual and long-term incentives. In addition, the Consultant analyzed the mix of pay elements, reviewed executive employment agreements and examined and reported on share usage and dilution, incentive and retention plan design and metrics and current executive compensation and regulatory trends that were relevant to Patriot. With the approval of the Compensation Committee, the Consultant also provided certain healthcare consulting services to the Company in 2012.

No member of the Compensation Committee or any of the named executive officers has any affiliation with the Consultant.

A substantial majority (93%) of the Company’s stockholders approved the executive compensation program described in the Company’s proxy statement filed in 2012. Certain elements of that program were not in effect in 2012 because of the Chapter 11 filing.

Benchmarking Process

Prior to the Chapter 11 Filing

Prior to the Chapter 11 filing, the Compensation Committee considered two peer groups, as well as broader market survey data, to compare compensation levels, elements, mix and trends in order to determine whether Patriot’s compensation programs were competitive and appropriate. The survey data was examined in conjunction with the data from both primary and secondary peer groups, with the primary peer group being the principal reference point and the secondary peer group being used to validate data from the primary peer group.

The primary peer group consists of eight publicly-traded coal companies: Alpha Natural Resources, Inc., Arch, Cloud Peak Energy, Inc., CONSOL Energy, Inc., James River Coal Company, Peabody, Walter Energy, Inc. and Westmoreland Coal Company.

Due to the modest size of the primary peer group, the Compensation Committee also analyzed compensation data from a second peer group. This second peer group consists of the companies in the primary peer group, plus eight companies that are similar in size to Patriot (based on revenues) and that have mineral or gas extraction businesses and substantial North American operations. These additional eight companies are: Cimarex Energy Company, Cliffs Natural Resources Inc., Compass Minerals International, Inc., Crosstex Energy, Inc., Martin Marietta Materials, Inc., Minerals Technologies, Inc., Newfield Exploration Company and Vulcan Materials Company.

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Because talent for certain key roles at Patriot can be acquired from a broad spectrum of companies, use of broader market surveys was also considered appropriate. The Compensation Committee utilized surveys such as the U.S. Mercer Benchmark Database Executive Survey Report, the Towers Watson Data Services Survey Report on Top Management Compensation and the Towers Watson U.S. Compensation General Industry Executive Database. The data from the published surveys was increased by 3% from the published date of the surveys to the various subsequent dates when the Compensation Committee reviewed the data, reflecting the Consultant’s estimate of the expected pay increases in 2012 for executives in the energy industry, based on a compilation of merit increase surveys.

Since the Chapter 11 Filing

Patriot has not engaged in any benchmarking of executive compensation since the Chapter 11 filing.

Considerations in Determining Compensation for 2012

Prior to the Chapter 11 Filing

Prior to the Chapter 11 filing, the Compensation Committee reviewed and considered the following information in establishing compensation for each named executive officer:

Overall, the Compensation Committee determined that Patriot’s executive compensation programs, as structured prior to the Chapter 11 filings, were consistent with the Compensation Committee’s executive compensation philosophy and guiding principles.

Since the Chapter 11 Filing

As discussed above, the named executive officers have not and will not receive any annual incentive awards or equity awards during the pendency of the Chapter 11 process, they are no longer eligible to participate in our Supplemental 401(k) Plan and, effective March 1, 2013, their base salaries were reduced by 2.5%. Due to these reductions, Patriot’s current named executive officers’ total cash compensation (salary plus annual incentive opportunity) and total direct compensation (salary plus annual incentive and long term incentive opportunities) rank approximately in the bottom 17th and 1st percentiles, respectively, compared to industry peers.

Employment Agreements and Organizational Changes

Prior to the Chapter 11 Filing

In the years prior to the Chapter 11 filing, Patriot entered into employment agreements with Messrs. Hatfield, Ebetino, Bean, Whiting, Engelhardt and Schroeder. The terms of each of these agreements were structured to attract and retain persons believed to be key to Patriot’s success and to be competitive with compensation practices for executives in similar positions at companies of similar size and complexity.

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Effective May 28, 2012, Mr. Whiting left the Company. Mr. Whiting had served as President, CEO and a member of the Board; Mr. Engelhardt, then Chairman of the Board, was appointed by the Board as CEO; and Mr. Hatfield, then Executive Vice President and Chief Operating Officer, was named President and Chief Operating Officer by the Board.

Since the Chapter 11 Filing

Effective September 21, 2012, Mr. Schroeder resigned from his position as Senior Vice President & CFO and assumed the new position of Senior Vice President of Financial Planning; and John E. Lushefski resigned from the Board and was appointed by the Board as Senior Vice President & CFO.

Effective October 23, 2012, Mr. Engelhardt resigned as CEO and Chairman of the Board; Mr. Hatfield was appointed President and CEO by the Board and was also appointed to serve on the Board; and Mr. Scharf was appointed Chairman of the Board.

Mr. Schroeder resigned as Senior Vice President of Financial Planning on November 2, 2012.

On January 11, 2013, the Bankruptcy Court entered an order approving Patriot’s rejection of its employment agreements (including the Company’s severance obligations thereunder) with Messrs. Whiting, Engelhardt and Schroeder.

Annual Base Salary

As noted above, annual base salary represents the primary component of compensation awarded to the named executive officers during the Chapter 11 proceedings. For the named executive officers, the Compensation Committee has historically awarded base salary increases (if any) after reviewing the Company’s performance, individual performance and competitive market compensation. The salaries of the named executive officers currently employed by Patriot (along with those of salaried employees generally) were decreased by 2.5% effective March 1, 2013.

Mr. Hatfield’s annual salary was increased from $600,000 to $675,000, effective May 28, 2012, and to $725,000, effective October 23, 2012, in connection with his promotions to the positions of President and Chief Operating Officer and President and CEO, respectively. These increases reflect the Compensation Committee’s determination of market pay for each of his two new positions, taking into account his experience, contributions and importance to Patriot. Mr. Hatfield’s current annual salary is $706,875, which reflects the 2.5% decrease for salaried employees effective March 1, 2013.

Mr. Bennett’s annual salary was increased from $396,550 to $435,800, effective September 1, 2012. This increase was made to recognize the importance of his position of Senior Vice President & Chief Marketing Officer and the contributions he is making to maintain Patriot’s customer relationships. Mr. Bennett’s current annual salary is $424,905, which reflects the 2.5% decrease for salaried employees effective March 1, 2013.

As of March 1, 2013, the annual salaries of the other named executive officers who are currently employed by Patriot were as follows: Mr. Lushefski – $560,625; Mr. Ebetino – $527,231; and Mr. Bean – $365,547. The salaries for these executives remained unchanged throughout 2012.

The 2012 annual salaries of the named executive officers no longer employed by the Company were as follows: Mr. Whiting – $805,000; Mr. Engelhardt – $725,000; and Mr. Schroeder – $486,675.

For the actual amounts of salary that the executives received in 2012, see the “Salary” column of the 2012 Summary Compensation Table below.

Prior to becoming executives, Messrs. Engelhardt and Lushefski also received customary director fees and deferred stock units for their service as directors in 2012.

The Compensation Committee will continue to review the base salaries of the named executive officers at least annually and may adjust such salaries to ensure that they are appropriate in the context of a Chapter 11 proceeding or competitive with those of peer executives at peer companies. Any future salary adjustments may also be based on factors such as an assessment of performance, experience, promotions and changes in level of responsibility, as well as the status of the Chapter 11 proceedings.

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Annual Management Incentive Plan

Patriot’s named executive officers and other designated key employees have historically participated in an annual incentive compensation plan. In general, Patriot’s annual incentive plan provided opportunities to earn annual cash incentive payments tied to the successful achievement of pre-established company and individual objectives that supported Patriot’s business strategy.

After the Chapter 11 filing, the annual incentive plan for 2012 was effectively terminated, as Patriot elected not to seek bankruptcy court approval for the plan. As a result, the named executive officers and other participants in the plan received no annual incentive awards for 2012, despite the fact that participants, including the named executive officers, earned awards totaling approximately $3 million under the plan.

Under the historical plan, the named executive officers were assigned threshold, target and maximum incentive payouts. If Patriot’s performance as measured against specified financial, safety and environmental objectives did not meet the threshold level established by the Compensation Committee, no incentive award would be earned with respect to those objectives. The incentive award that could be earned equaled 50% of the target payout at threshold levels and was capped at 175% to 200% of the target payout (depending upon the named executive officer) for performance at or above maximum levels. The target payouts for the named executive officers were established considering the importance of the objectives to Patriot’s strategy and through an analysis of compensation for comparable positions at Patriot’s peer companies in order to provide a competitive level of compensation for achieving the applicable performance objectives.

2012 Annual Incentive Measures and Payouts

At the beginning of 2012, the Compensation Committee set the annual incentive plan metrics listed below. As noted above, the plan was terminated following the Chapter 11 filing and no payments were made under the plan for 2012, although certain plan metrics were satisfied.

The chart below sets forth relevant performance objectives for each metric for 2012 (excluding individual performance).

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Prior to the Chapter 11 filing, the named executive officers’ threshold, target and maximum incentive opportunities for 2012, as a percentage of their salaries, based on achievement of relevant Patriot performance objectives, were as follows:

Named executive officers presently employed by Patriot:

Named executive officers formerly employed by Patriot:

Clawback Policy

On January 27, 2010, the Compensation Committee adopted a policy authorizing Patriot to recover cash bonuses paid to executive officers under certain circumstances. The policy provides that if Patriot restates its financial results under the U.S. securities laws as a result of deliberate misconduct or fraud by an executive officer, then to the extent permitted under applicable law, Patriot will be entitled to recover any cash bonus paid to that executive officer that (i) was paid in the 12 months prior to the first filing of the restated financial results, and (ii) was higher than it would have been had the original financial statements not been affected by the misconduct or fraud. The policy authorizes the Board to exercise its business judgment to determine the appropriate amount and most cost-effective method of any such recovery, including direct repayment of the cash bonus by the executive officer, or an offset against other amounts owed to or to be paid to the executive officer by Patriot.

Long-Term Incentives

In 2007, in connection with Patriot’s spin-off from Peabody, the Board adopted the LTIP, which was approved by Patriot’s sole stockholder at that time. In 2009, the Company’s stockholders approved the LTIP. Awards under the LTIP have historically provided opportunities for the named executive officers and other key employees to earn equity awards based upon successful achievement of pre-established long-term (i.e., greater than one-year) objectives, increases in Patriot’s stock price, continued service with Patriot or any combination of these factors.

Following the Chapter 11 filing, the Company suspended the LTIP and anticipates that as part of the bankruptcy process it will terminate the LTIP and cancel outstanding equity awards granted thereunder, and therefore will not grant any new equity awards or issue any shares on settlement or exercise of outstanding equity awards. Since the Chapter 11 filing, the executives have received no LTIP awards, and they are expected to realize little or no value from the outstanding LTIP awards that they previously received. The executives’ stock options are significantly underwater and the value of their other awards (restricted stock, restricted stock units and/or deferred stock units) has declined precipitously since their grant dates (to $0.07 for each share of Patriot Common Stock underlying the awards as of December 31, 2012).

Prior to the Chapter 11 filing, other than to satisfy tax withholding obligations upon the vesting of equity awards, only one of the named executive officers ever sold any shares of Patriot Common Stock (i.e., Rule 10b-5 sales totaling 27,143 shares in 2010 and 2011).

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Pre-Chapter 11 Filing Policy on Grant of Equity-Based Compensation

In January 2008, the Compensation Committee approved a general policy for granting equity-based compensation (the “Regular Grant Policy”), which was subject to modification from time to time as deemed appropriate by the Compensation Committee. The Compensation Committee historically granted equity-based compensation to attract, motivate, compensate and retain executive officers and other key employees and to align their interests with the interests of stockholders. The timing of grants of equity-based compensation was designed to achieve these purposes. The following describes the pre-Chapter 11 filing process for making equity-based compensation grants, as set forth in the Regular Grant Policy.

At the regularly scheduled meeting of the Compensation Committee held in December of each year, the Compensation Committee reviewed the performance of the Company and its executive officers during the fiscal year. Based upon that review and such other factors as the Compensation Committee determined relevant, including analyses provided by the Consultant, the Compensation Committee granted equity-based compensation to executive officers and other eligible employees by approving either (i) the terms of specific grants or (ii) a specific formula for determination of the terms of the grants. Under the Regular Grant Policy, such grants were made effective the first business day in January of the following year and determined based on the closing price of Patriot Common Stock as reported on the NYSE on such day or the last preceding day on which a sale was reported (the “fair market value”).

The Compensation Committee approved all grants of equity-based compensation to eligible newly-hired or promoted employees, or made under or in connection with retention agreements or for other valid business purposes. Such grants were approved at a regular or special meeting of the Compensation Committee that occurred on or prior to the date on which the award was considered to be granted.

All stock options were granted at an option price not less than the fair market value of the stock on the grant date. The grant date of any award was the date of the meeting of the Compensation Committee approving the grant or any later grant date approved by the Compensation Committee.

Extended Long-Term Incentive Awards

At the time of the spin-off from Peabody, a one-time long-term incentive award (the “Extended Long-Term Incentive Award”) intended to promote long-term employee retention and achievement of certain financial objectives was made to Messrs. Whiting, Schroeder, Bean and Ebetino, as well as other key employees. Upon joining the Company in July 2008, Mr. Bennett received an Extended Long-Term Incentive Award subject to the same terms and conditions as the awards made to the other named executive officers at the time of the spin-off. Messrs. Hatfield, Engelhardt and Lushefski did not participate in the Extended Long-Term Incentive Award Program. Other than in the event of death, disability or a change of control of Patriot, the service condition of the Extended Long-Term Incentive Awards was not scheduled to be met prior to November 1, 2012. In addition, the performance condition of the awards was scheduled to be met only if certain performance metrics were achieved. The awards were subject to forfeiture in the event of termination of employment for any reason prior to vesting. These vesting schedules were designed to reinforce the recipients’ long-term commitment to Patriot.

As a result of the Chapter 11 filing, the Company suspended the Extended Long-Term Incentive Award Program, and no shares were issued under the awards on the scheduled vesting date of November 1, 2012.

Annual Long-Term Incentive Awards

Prior to the Chapter 11 filing, through Patriot’s annual long-term incentive awards, a competitive long-term incentive opportunity was available to each of Patriot’s named executive officers and certain other key employees. The timing, form and amount of such awards were largely determined by the named executive officer’s employment agreement, if applicable, peer group analysis and a comparison of such awards to the awards of the other named executive officers.

Certain of the named executive officers received annual long-term incentive awards each January with a value at least equal to the percentage of their base salaries set forth below. Awards in these percentages were made in January 2012 to the individuals who were named executive officers at the time, as listed below. Other than for increases due to promotions, these percentages were unchanged since 2009.

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Named executive officers presently employed by Patriot (1):

Named executive officers formerly employed by Patriot (1):

In order to maintain the emphasis on performance-based pay, the Compensation Committee, as it had done in prior years, adopted a balanced, performance-oriented approach when granting annual long-term incentive awards to the named executive officers. On January 3, 2012, each of Messrs. Whiting, Hatfield, Schroeder, Ebetino, Bennett, and Bean received an annual equity award comprised of:

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Each type of long-term incentive award was intended to promote executive officer retention, align executive officer and stockholder interests, provide executive officers with stock ownership in Patriot and motivate executive officers to increase the price of Patriot Common Stock.

As discussed above in connection with the Compensation Committee’s decision to emphasize performance-based pay, on January 3, 2010, the Compensation Committee made the second in a series of performance share grants covering a three-year performance cycle. The second cycle was for 36 months, beginning on January 3, 2010. Performance was to be measured based on the Company achieving specified levels of TSR compared to the then primary peer group. That cycle was to end on December 31, 2012, but the Company has suspended these awards and no shares were issued with respect to the awards.

In addition to the above annual long-term incentive awards, Mr. Engelhardt received 100,000 restricted stock units upon being named CEO in May 2012, which were scheduled to vest in one-third increments on May 28 of each of 2013, 2014 and 2015. Mr. Engelhardt forfeited these shares upon his resignation as CEO in October 2012. Mr. Hatfield received 281,250 restricted stock units upon being named President and Chief Operating Officer in May 2012, which are subject to the same vesting schedule as applied to Mr. Engelhardt’s restricted stock units. As with other awards granted to the named executives before the Chapter 11 filing, the value of these awards has declined from $2.60 per share as of the grant date to $0.07 per share as of December 31, 2012. As the Company has suspended the LTIP and anticipates that as part of the bankruptcy process it will terminate the LTIP and cancel outstanding equity awards granted thereunder, Messrs. Hatfield and Engelhardt are unlikely to ever receive these restricted stock units.

Mr. Lushefski did not receive any long-term incentive awards in connection with his appointment as Senior Vice President & CFO in September 2012.

Retirement Benefits

Defined Contribution Plan

Patriot maintains a tax-qualified defined contribution retirement plan (“401(k) Plan”) for its employees. Named executive officers participate in this plan while employed by the Company on the same terms as other eligible employees, subject to any legal limits on the amounts that may be contributed by or paid to such named executive officers under the plans.

Excess Defined Contribution Retirement Plan

Since the spin-off from Peabody, the Company has maintained the Supplemental 401(k) Plan, a non-qualified excess defined contribution plan that provides retirement benefits to executive officers (including the named executive officers) whose pay exceeds legislative limits for qualified benefit plans. The Supplemental 401(k) Plan was suspended, effective December 28, 2012, and an order authorizing Patriot to terminate the plan was granted by the Bankruptcy Court on March 15, 2013. Most of the participants’ retirement savings previously contributed to the plan are attributable to pre-petition service and therefore will be treated as pre-petition general unsecured claims against the bankruptcy estates of Patriot and its affiliates, subject to compromise.

Tax Gross-Ups

Mr. Ebetino and Mr. Bean are entitled pursuant to their employment agreements to be reimbursed (grossed up) for the excise tax payable if they receive “excess” payments in connection with a change of control of the Company. No other employee of the Company is entitled to receive tax gross-ups from the Company, and the Company does not intend to grant additional tax gross-ups in the future.

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Other Benefits Provided by the Company

The named executive officers receive the same health and welfare and fringe benefits as all other salaried employees of Patriot. The Company has already reduced some of these benefits and other such benefits could be reduced or terminated in 2013.

Perquisites

Due to Mr. Lushefski’s principal residence being in New Jersey, the Company provides him with housing in the St. Louis area and use of a vehicle, and also pays for Mr. Lushefski’s travel expenses from his home in New Jersey to the Company’s offices in St. Louis.

Patriot does not provide any perquisites that exceed $10,000 per year to any other of its named executive officers or other executive officers.

Stock Ownership Guidelines

Prior to the Chapter 11 filing, the Board had established stock ownership guidelines for Patriot’s executive officers and directors to further align their interests with those of stockholders. Those guidelines have been suspended because of the Chapter 11 filing.

Deductibility of Compensation Expenses

Pursuant to Section 162(m) (“Section 162(m)”) of the Internal Revenue Code of 1986, as amended (the “IRC”), compensation paid to each of the CEO and the three other most highly compensated executive officers in excess of $1 million per year generally is not tax deductible, except to the extent such excess constitutes performance-based compensation. One requirement for establishing performance-based compensation under Section 162(m) is that the material terms of the performance goals under which the compensation is provided be approved by stockholders at least once every five years. At the 2009 stockholders’ meeting, the Company’s stockholders approved the material terms of the performance goals under both the annual incentive plan and the LTIP. The Compensation Committee considers its primary goal to design compensation strategies that further the economic interests of the Company and its stockholders. In certain cases, the Compensation Committee may determine that the amount of tax deductions lost is outweighed by the potential opportunity a compensation program provides for creating stockholder value. The Compensation Committee therefore retains the ability to evaluate the performance of the Company’s executive officers and to pay appropriate compensation, even if it may result in the non-deductibility of certain compensation.

Actual Compensation for 2012 versus Compensation Reported in 2012 Summary Compensation Table

The 2012 Actual Compensation Table below summarizes the named executive officers’ actual compensation for the fiscal year ended December 31, 2012, as defined below. The named executive officers’ actual compensation for 2012 was considerably lower than the total compensation reported as paid to the executives for 2012 in the 2012 Summary Compensation Table below. This difference is primarily due to the requirement under the SEC’s disclosure rules to report in the Stock Awards and Option Awards columns of the 2012 Summary Compensation Table the value of the equity awards granted to the named executive officers in 2012 based on the price of Patriot Common Stock on the applicable grant dates. These awards were granted to the executives prior to the Chapter 11 filing on dates on which the price of Patriot Common Stock ranged from $2.60 to $9.13. The price of Patriot Common Stock was $0.07 on December 31, 2012, reflecting a decrease of between 97% and 99% from the grant date prices. Because of the impact of this decrease on the value of the equity awards granted to the named executive officers in 2012, we believe that the 2012 Actual Compensation Table more accurately reflects the executives’ compensation for 2012.

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For purposes of the 2012 Actual Compensation Table, actual compensation is defined to include the following:

Even the relatively modest values for the equity awards included in the table likely overstate the amounts, if any, that the named executive officers will ultimately realize from the awards. Due to the Chapter 11 filing, there is significant uncertainty regarding the value of our equity securities, including our Common Stock and equity awards that are settled in or exercisable for our Common Stock. Under the priority rankings established by the Bankruptcy Code, unless creditors agree otherwise, pre-petition and post-petition liabilities must be satisfied in full before stockholders are entitled to receive any distribution or retain any property under a plan of reorganization. We have suspended the LTIP and we do not anticipate issuing any shares on settlement or exercise of outstanding equity awards, including awards held by our named executive officers.

2012 ACTUAL COMPENSATION TABLE

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REPORT OF THE COMPENSATION COMMITTEE

The Compensation Committee has reviewed and discussed with management the Company’s disclosures under “Compensation Discussion and Analysis,” beginning on page 3 of this Amendment.

Based on such review and discussion, the Compensation Committee recommended to the Board that the Compensation Discussion and Analysis be included in this Amendment and incorporated by reference in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2012 for filing with the Securities and Exchange Commission.

MEMBERS OF THE COMPENSATION COMMITTEE:

MICHAEL P. JOHNSON, CHAIR

J. JOE ADORJAN

B. R. BROWN

ROBERT O. VIETS

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2012 SUMMARY COMPENSATION TABLE

The following table summarizes the total compensation paid to the named executive officers for the fiscal year ended December 31, 2012. The amounts shown in the “Stock Awards” and “Option Awards” columns in the table below are not the amounts actually realized by the named executive officers for their equity awards. As required by the rules of the SEC, the amounts instead represent the aggregate grant date fair value of the awards. These awards represent customary annual awards given to the Company’s executives prior to the Chapter 11 filing in accordance with the Company’s executive compensation philosophy and objectives. Given the bankruptcy process, the significant decline in the value of Patriot Common Stock since the Chapter 11 filing and the suspension of the LTIP, the executives are expected to realize little or no value from these awards. Prior to the Chapter 11 filing, other than to satisfy tax withholding obligations upon the vesting of equity awards, only one of the named executive officers ever sold any shares of Patriot Common Stock (i.e., Rule 10b-5 sales totaling 27,143 shares in 2010 and 2011). Accordingly, with respect to the stock awards shown in the table below, the executives have generally realized limited benefits from these stock awards and are unlikely to realize any meaningful value from these stock awards in the future.

Please see the 2012 Actual Compensation Table above for the amounts of the named executive officers’ compensation for 2012, as valued based on the $0.07 closing share price on December 31, 2012.

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GRANTS OF PLAN-BASED AWARDS IN 2012

The following table sets forth information concerning the grants of awards to each of the Company’s named executive officers for the period January 1, 2012 through December 31, 2012. SEC rules require us to report plan-based awards made in 2012 at their fair value as of the grant date regardless of the value of the awards as of December 31, 2012. The awards reflected in the table below represent customary annual awards given to the Company’s executives prior to the Chapter 11 filing in accordance with the Company’s executive compensation philosophy and objectives. The table and related disclosures do not take into account the effects of the following

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The Company has entered into employment agreements with Messrs. Hatfield, Ebetino, Bean, Whiting, Engelhardt and Schroeder. Pursuant to the terms of these agreements, these executives are entitled to specified levels of base salary and annual and long-term incentive opportunities. The compensation levels for each such executive as of December 31, 2012 are shown under the captions “Annual Base Salary,” “Annual Management Incentive Plan” and “Long-Term Incentives” on page 9 through 13 of this Amendment. On January 11, 2013, the Bankruptcy Court entered an order approving Patriot’s motion to reject the employment agreements with Messrs. Whiting, Engelhardt and Schroeder (including the Company’s obligations thereunder with respect to base salary, annual and long-term incentive opportunities and severance).

OUTSTANDING EQUITY AWARDS AT 2012 FISCAL YEAR-END

The following table sets forth detail about the outstanding equity awards for each of the named executive officers as of December 31, 2012. Under SEC rules, we are required to provide information regarding unexercised options, restricted stock that has not vested and outstanding equity incentive plan awards, regardless of the current value of these awards as of December 31, 2012. The awards reflected in the table below represent customary annual awards given to the Company’s executives prior to the Chapter 11 filing in accordance with the Company’s executive compensation philosophy and objectives. Given the Chapter 11 filing and the price of Patriot Common Stock as of the date of this Amendment, the executives are expected to realize little or no value from the equity awards shown in the table below. In addition, following the Chapter 11 filing, the Company suspended the LTIP and anticipates that as part of the bankruptcy process it will terminate the LTIP and cancel outstanding equity awards granted thereunder and therefore will not grant any new equity awards or issue any shares on settlement or exercise of outstanding equity awards.

The table does not reflect performance-based restricted stock unit awards that were scheduled to vest in 2012 but that were not distributed as a result of the suspension of the LTIP. Although the Company did not determine whether these awards met the applicable performance criteria, it is highly unlikely that the threshold performance goals were achieved. The table does, however, include performance-based restricted unit awards that are not yet scheduled to vest, although it is highly unlikely that the threshold performance goals applicable to the awards will be achieved.

All of Messrs. Whiting’s, Engelhardt’s and Schroeder’s unvested equity awards were forfeited upon their respective departures from the Company, except for 33,165 shares of restricted stock and 97,494 stock options that accelerated upon Mr. Whiting’s departure pursuant to the terms of his award agreements. Messrs. Whiting and Schroeder also hold stock options that vested prior to their departure. All of the options held by Messrs. Whiting and Schroeder are significantly underwater, and the Company has determined not to honor any stock option exercises.

Unexercisable options and unvested restricted stock or time-based restricted stock units reflected in the table below vest in full upon death or disability or a change of control of the Company. Except as noted in footnotes 10, 11, 13, 14, 17 and 18 below, all unexercisable options and unvested restricted stock or time-based restricted stock units reflected in the table below are subject to forfeiture if the holder terminates employment for any reason other than death or disability. Except as noted in footnotes 12 and 15 below, unvested performance-based restricted stock units are subject to forfeiture if the holder terminates employment for any reason.

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